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(-) Description

Title :  STRUCTURE OF XANTHOMONAS CAMPESTRIS EFFECTOR PROTEIN XOPD BOUND TO TOMATO SUMO
 
Authors :  J. N. Pruneda, D. Komander
Date :  03 May 16  (Deposition) - 27 Jul 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme, Ce Clan, Deubiquitinase, Desumoylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Pruneda, C. H. Durkin, P. P. Geurink, H. Ovaa, B. Santhanam, D. W. Holden, D. Komander
The Molecular Basis For Ubiquitin And Ubiquitin-Like Specificities In Bacterial Effector Proteases.
Mol. Cell V. 63 261 2016
PubMed-ID: 27425412  |  Reference-DOI: 10.1016/J.MOLCEL.2016.06.015

(-) Compounds

Molecule 1 - XANTHOMONAS OUTER PROTEIN D
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 298-515
    Gene: XOPD, XCV0437
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. VESICATORIA (STRAIN 85-10)
    Organism Taxid: 316273
 
Molecule 2 - SMALL UBIQUITIN-RELATED MODIFIER
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SUMO
    Organism Common: TOMATO
    Organism Scientific: SOLANUM LYCOPERSICUM
    Organism Taxid: 4081
    Synonym: SUMO

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1AYE1Mod. Amino AcidPROP-2-EN-1-AMINE
2D1D1Ligand/Ion(4S,5S)-1,2-DITHIANE-4,5-DIOL
3MLI2Ligand/IonMALONATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:434 , GLU A:458 , MET A:459 , PRO A:460binding site for residue MLI A 601
2AC2SOFTWARETYR A:440 , HOH A:703binding site for residue D1D A 602
3AC3SOFTWAREGLY A:342 , ILE B:61 , ALA B:62 , ARG B:69 , ARG B:71 , HIS B:92 , HOH B:202 , HOH B:206 , HOH B:213 , HOH B:231 , HOH B:236binding site for residue MLI B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JP1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JP1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JP1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JP1)

(-) Exons   (0, 0)

(no "Exon" information available for 5JP1)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eehhhhhhhhhhhhhhhh...hhh.eee.hhhhhhhh...hhhhhhhhhhhhhh.....eeeeeeee...eeeeeeee.......eeeee......hhhhhhhhhhhhhhh..hhhhhee..........hhhhhhhhhhhhhhhhhhh................hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jp1 A 317 DNLPSPQDVADPELPPVRATSWLLDGHLRAYTDDLARRLRGEPNAHLLHFADSQVVTMLSSADPDQQARAQRLLAGDDIPPIVFLPINQPNAHWSLLVVDRRNKDAVAAYHYDSMAQKDPQQRYLADMAAYHLGLDYQQTHEMPIAIQSDGYSCGDHVLTGIEVLAHRVLDGTFDYAGGRDLTDIEPDRGLIRDRLAQA 515
                                   326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506         


Chain B from PDB  Type:PROTEIN  Length:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.....eeeeeee....hhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 5jp1 B  19 VHINLKVKGQDGNEVFFRIKRSTQMRKLMNAYCDRQSVDMNSIAFLFDGRRLRAEQTPDELEMEEGDEIDAMLHQTGx  96
                                    28        38        48        58        68        78        88       |
                                                                                                        96-AYE
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5JP1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JP1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JP1)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        Q3BYJ5_XANC5 | Q3BYJ5: 2oiv 2oix 5jp3

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